Summary Non-melanoma skin cancer, which includes basal cell carcinoma and squamous cell carcinoma (SCC), is the most common malignancy in the Western world. Our published work has shown that cancer susceptibility genes for SCC exhibit preferential allelic imbalance in tumors providing a strategy to identify these alleles. Ou initial allelic imbalance studies used sets of multiple SCCs from immunosuppressed transplant recipients in low-resolution genotyping screens to identify candidate susceptibility loci. Our data have revealed multiple loci showing evidence of allele-specific imbalance (ASI). Subsequent high-resolution quantitative genotyping across a 9-Mb candidate locus on 11q24 in matched normal and tumor DNAs from both sporadic patients and transplant recipients led to the identification of variants mapping to a 160kb region on 11q24 that show significant evidence for ASI. This study will determine if ASI mapping is a useful strategy for the identification of cancer risk alleles. Furthermore, we will test the hypothesis that allelic variations within our minimal candidate locus on 11q24 are associated with an increased risk of developing cSCC in the following two aims: 1. To characterize genetic diversity at our minimal locus on 11q24 in order to identify variants driving the observed allele specific imbalance. We propose that allelic versions of the functional unit (gene, regulatory region, non-coding RNA) driving preferential allelic loss t 11q24 will have stronger tumor-suppressing abilities than other alleles. To identify candidate causal variants, we will map all allelic variants in tumors showing ASI by targeted deep-sequencing of 11q24 and then will perform in silico studies to assess potential function(s) of alleles showing ASI. 2. To test variants at 11q24 for susceptibility to cSCC in order to identify genotypes that predispose humans to cSCC. We will test whether variants at 11q24 showing preferential allelic imbalance in tumors are associated with the risk of developing SCC. We will genotype ten variants from this locus that show significant evidence of ASI in 300 SCC cases and 300 controls. Top variants showing evidence of risk will be validated in over 1650 additional SCC cases and 1800 controls. Results from this study will determine if the use of ASI mapping is another strategy for the identification of cancer risk alleles. The long-term goals of these studies are to understand the mechanisms by which the variants at 11q24 contribute to SCC tumorigenesis and risk and to evaluate their candidacy for therapeutic or preventative strategies for cutaneous SCC. These studies have high impact as they validate allele-specific imbalance as a method to identify genes and susceptibility alleles important in cancer and have the potential to identify new genes important in SCC.